Find research datasets worth reusing
Search datasets from major research repositories and use ShareScore to quickly assess how well each record supports discovery, access, and reuse.
861
datasets available to search
ShareScore release 0.9.0
Dataset results
861 results for “collagen I”
Hypoxia preconditioned mesenchymal stem cells prevent cardiac fibroblast activation and collagen production via leptin
Open the record for dataset details and reuse information.
MALDI-TOF-MS reference spectra and sequence data for African bovid collagen for Zooarchaeology by Mass Spectrometry (ZooMS)
<p>MALDI-TOF-MS spectra of extracted collagen from modern African bovids used as reference spectra to develop markers for Zooarchaeology by Mass Spectrometry (ZooMS). Some of this material was also analyzed by LC-MS/MS. That data can be found at MassIVE MSV000084675 (<a href="https://doi.org/doi:10.25345/C5239K">doi:10.25345/C5239K</a>). Information about the species of the samples can be found in Key for Labels.csv file.</p> <p>The sequence data contains annotated alignments of the proteins COL1A1 and COL1A2 and the alignments for the available bovid collagen protein sequences. More information on these files can be found in the corresponding manuscript to this dataset.</p>
Data from: Biologically and diagenetically derived peptide modifications in Moa collagens
The modifications that occur on proteins in natural environments over time are not well studied, yet characterizing them is vital to correctly interpret sequence data recovered from fossils. The recently extinct moa (Dinornithidae) is an excellent candidate for investigating the preservation of proteins, their post-translational modifications (PTMs) and diagenetic alterations during degradation. Moa protein extracts were analysed using mass spectrometry, and peptides from collagen I, collagen II and collagen V were identified. We also identified biologically derived PTMs (i.e. methylation, di-methylation, alkylation, hydroxylation, fucosylation) on amino acids at locations consistent with extant proteins. In addition to these in vivo modifications, we detected novel modifications that are probably diagenetically derived. These include loss of hydroxylation/glutamic semialdehyde, carboxymethyllysine and peptide backbone cleavage, as well as previously noted deamidation. Moa collagen sequences and modifications provide a baseline by which to evaluate proteomic studies of other fossils, and a framework for defining the molecular relationship of moa to other closely related taxa.
Data from: Collagen vitrigel promotes hepatocytic differentiation of induced pluripotent stem cells into functional hepatocyte-like cells
Differentiation of stem cells to hepatocytes provides an unlimited supply of human hepatocytes and therefore has been vigorously studied. However, to date, the stem cell-derived hepatocytes were suggested to be of immature features. To obtain matured hepatocytes from stem cells, we tested the effect of culturing iPS cell-derived endoderm cells on collagen vitrigel membrane and compared with our previous reported nanofiber matrix. We cultured hiPS cell-derived endoderm cells on a collagen vitrigel membrane and examined the expression profiles, and tested the activity of metabolic enzymes. Gene expression profile analysis of hepatocytic differentiation markers revealed that upon culture on collagen vitrigel membrane, immature markers of AFP decreased, with a concomitant increase in the expression of mature hepatocyte transcription factors and mature hepatocyte markers such as ALB, ASGR1. Mature markers involved in liver functions, such as transporters, cytochrome P450 enzymes, phase II metabolic enzymes were also upregulated. We observed the upregulation of the liver markers for at least 2 weeks. Gene array profiling analysis revealed that hiPS cell-derived hepatocyte-like cells (hiPS-hep) resemble that of the primary hepatocytes. Functions of the CYP enzyme activities were tested in multi-institution and all revealed high CYP1A, CYP2C19, CYP2D6, CYP3A activity, which could be maintained for at least 2 weeks in culture. Taken together, the present approach identified that collagen vitrigel membrane provides a suitable environment for the generation of hepatocytes from hiPS cells that resemble many characteristics of primary human hepatocytes.
MALDI-TOF MS spectra and sequence data of collagen of modern and archaeological flatfish from European waters
<p>MALDI-TOF MS spectra, LC-MS/MS datafiles, and Mascot MZID files of modern bone collagen of 18 species of Pleuronectiformes as reference spectra that were used to develop peptide biomarkers for ZooMS (Zooarchaeology by Mass Spectrometry). Details on the samples used can be found in the file "Reference spectra information.csv". Further information on the method and results can be found in the manuscript. The file names contain the type of data file and the species name. </p> <p>MALDI-TOF MS of 202 archaeological samples for Zooarchaeology by Mass Spectrometry (ZooMS) from three case study sites from around the North Sea: Barreau Saint-George ferroviaire in northern France, and 16-22 Coppergate and Blue Bridge Lane from York in the United Kingdom. Details on the samples can be found in the supplementary information of the manuscript. Further information on the method can be found in the manuscript. The file names are labeled with the sample ID number and the triplicate number (out of 3).</p>
Investigating species composition in the Early Aurignacian of Le Piage (France) through collagen fingerprinting (ZooMS) of screen-recovered small bone fragments
<p>This link supplements the paper "Investigating species composition in the Early Aurignacian of Le Piage (France) through collagen fingerprinting (ZooMS) of screen-recovered small bone fragments" published in Paleoanthropology (https://paleoanthropology.org/ojs/index.php/paleo)</p> <p>We analysed with ZooMS (Zooarchaeology by mass Spectrometry) 1,050 bone fragments recovered through water sieving from an Early Aurignacian layer (37–34 ka cal. BP) in the site of Le Piage (Lot, France) to compare the taxonomic identifications of bone remains using traditional morphological attributes with remains identified using ZooMS, and discuss the implications of the taxonomic patterns that we uncovered. </p> <p>This page contains mzXml files of the spectra obtained and analysed within the scope of the published paper. The files are classified by runs, and the excel sheet entitled "Sample location (spectrum n°) in MS analyses" stipulates which mzXML files correspond to which specimen. This page also contains the simplified database reporting the identifications obtained through peptide mass fingerprinting (PMF) and a breakdown of deamidation values calculated with the Betacalc 3 published in Wilson et al. (2012).</p> <p><span><span>For any questions please contact Pauline Raymond (pauline.raymond@college-de-france.fr).</span><br><span>Please use the DOI when citing this dataset. </span></span></p>
Data for publication: "Plasma-Activated Polydimethylsiloxane Microstructured Pattern with Collagen for Improved Myoblast Cell Guidance"
<p>Abstract</p> <p>We focused on polydimethylsiloxane (PDMS) as a substrate for replication, micropatterning, and construction of biologically active surfaces. The novelty of this study is based on the combination of the argon plasma exposure of a micropatterned PDMS scaffold, where the plasma served as a strong tool for subsequent grafting of collagen coatings and their application as cell growth scaffolds, where the standard was significantly exceeded. As part of the scaffold design, templates with a patterned microstructure of different dimensions (50 × 50, 50 × 20, and 30 × 30 μm2) were created by photolithography followed by pattern replication on a PDMS polymer substrate. Subsequently, the prepared microstructured PDMS replicas were coated with a type I collagen layer. The sample preparation was followed by the characterization of material surface properties using various analytical techniques, including scanning electron microscopy (SEM), energy-dispersive X-ray spectroscopy (EDS), and X-ray photoelectron spectroscopy (XPS). To evaluate the biocompatibility of the produced samples, we conducted studies on the interactions between selected polymer replicas and micro- and nanostructures and mammalian cells. Specifically, we utilized mouse myoblasts (C2C12), and our results demonstrate that we achieved excellent cell alignment in conjunction with the development of a cytocompatible surface. Consequently, the outcomes of this research contribute to an enhanced comprehension of surface properties and interactions between structured polymers and mammalian cells. The use of periodic microstructures has the potential to advance the creation of novel materials and scaffolds in tissue engineering. These materials exhibit exceptional biocompatibility and possess the capacity to promote cell adhesion and growth.</p> <p> </p>
Increased spatial coupling of integrin and collagen IV in the immunoresistant clear-cell renal-cell carcinoma tumor microenvironment - Validation mIF
<p>mIF object from <em>spatialTIME</em> R package, calculating univariate Ripley's K on multiplex immunofluorescence images stained with FOXP3, CD8, CD68, ITGAV, COL4, VIM, SMA, and PCK. Data was processed with InForm and HALO. </p> <p>Clear cell renal cell carcinoma and papillary renal cell carcinoma were profiled before and after exposure to immunotherapy, with and without sarcomatoid features in clear cell tumors. Each tumor had a field of view in the stromal compartment and field of view in the tumor compartment.</p> <p>For appropriate clinical information associated with this study, please contact Dr. Brandon Manley.</p>
Raw mass spectrometry data for "Lysyl hydroxylase 2 mediated collagen post-translational modifications and functional outcomes"
<p><strong>Abstract:</strong> Lysyl hydroxylase 2 (LH2) is a member of LH family of enzymes (LH1-3) that catalyze the hydroxylation<br> of lysine (Lys) residues on collagen, and this particular isozyme has been implicated in Bruck syndrome,<br> fibrosis and cancer metastasis. Previously, we proposed LH2 as a telopeptidyl LH for type I collagen and<br> this specific function is now generally accepted. However, several fundamental questions remain<br> unanswered: 1, Is LH2 responsible for both N- (α1 and 2 chains) and C-telopeptidyl (α1 chain) Lys<br> hydroxylation? 2, Is LH2 involved in the helical Lys hydroxylation? 3, what are the functional<br> consequences when LH2 is completely lacking? To answer these questions, we generated LH2-null MC3T3<br> cells (LH2 KO) using CRISPR/Cas9, and extensively characterized the molecular and fibrillar phenotypes<br> of type I collagen. Cross-link analysis demonstrated that the hydroxylysine-aldehyde (Hyl<sup>ald</sup>)-derived crosslinks<br> were completely absent from LH2 KO collagen with concomitant increases in the Lys<sup>ald</sup>-derived crosslinks.<br> Mass spectrometric analysis revealed that, in LH2 KO type I collagen, telopeptidyl Lys hydroxylation<br> was completely abolished at all sites while helical Lys hydroxylation was slightly diminished in a sitespecific<br> manner. Moreover, di-glycosylated Hyl was diminished at the expense of mono-glycosylated Hyl.<br> Furthermore, prolyl 3-hydroxylation was slightly increased in LH2 KO type I collagen. In LH2 KO samples,<br> collagen solubility was markedly increased, fibril diameters are significantly diminished, and<br> mineralization severely impaired. Together, these data underscore the critical role of LH2-catalyzed<br> collagen modifications and consequent cross-linking in matrix stability, organization and mineralization.</p>
Veritas Collagen Matrix Cystocele Repair Study - Postmarketing
ClinicalTrials.gov study NCT00860912. IPD Sharing: NO. Countries: 0. Publications: 1.
Efficacy and Safety of A Collagen Bupivacaine Implant in Patients After Gastrointestinal Surgery
ClinicalTrials.gov study NCT00661466. IPD Sharing: Not stated. Countries: 1. Publications: 0.
Using of Collagen Matrix for Maxillary Tuberosity Donor Area Preservation
ClinicalTrials.gov study NCT06039839. IPD Sharing: NO. Countries: 1. Publications: 0.
CTG Versus Collagen Matrix for Peri-Implant Soft Tissue Augmentation
ClinicalTrials.gov study NCT07371481. IPD Sharing: NO. Countries: 1. Publications: 0.
Peri-Strips Dry (PSD) Veritas Collagen Matrix Staple Line Reinforcement for Colorectal Surgery
ClinicalTrials.gov study NCT00559013. IPD Sharing: Not stated. Countries: 1. Publications: 0.
MyoRing Implantation With Corneal Collagen Crosslinking for Keratoconus
ClinicalTrials.gov study NCT02590549. IPD Sharing: Not stated. Countries: 0. Publications: 1.
Assessment of Corneal Endothelium After Collagen Cross Linking
ClinicalTrials.gov study NCT04160338. IPD Sharing: Not stated. Countries: 0. Publications: 9.
VisR Ultrasound for Noninvasively Interrogating Stromal Collagen Organization in Women as a Breast Cancer Biomarker: Evaluation of Anisotropy in Cancer Patients
ClinicalTrials.gov study NCT06878547. IPD Sharing: YES. Countries: 1. Publications: 0.
IMPACT OF SUPPLEMENTATION WITH LOW MOLECULAR WEIGHT HYDROLYZED COLLAGEN AND VERISOL ON THE EXPRESSION OF LINES, SKIN QUALITY, AND LEVELS OF KLOTHO, VEGF, AND TGF-BETA IN THE EYE REGION
ClinicalTrials.gov study NCT06971029. IPD Sharing: NO. Countries: 0. Publications: 2.
VisR for Noninvasively Interrogating Stromal Collagen Organization as a Breast Cancer Biomarker: Evaluation of Compression in Control Subjects
ClinicalTrials.gov study NCT06547034. IPD Sharing: YES. Countries: 1. Publications: 0.
Clinical and Histological Outcomes of Using Collagen Matrix or Soft Tissue Graft Around Implants
ClinicalTrials.gov study NCT05123898. IPD Sharing: NO. Countries: 1. Publications: 0.
ScienceDex guides
Understand access before you commit
These curated guides explain access requirements, typical timelines, costs, and reuse considerations for widely used research datasets.
Allen Brain Atlas
Allen Brain Atlas is an Allen Institute collection of brain map atlases, datasets, APIs, and analysis tools covering mouse, human, and non-human primate brain resources.
Annotated Behaviour and Observability Dataset (ABODe)
ABODe is a University of Edinburgh DataShare dataset for behavior classification in group-housed mice using home-cage video, identities, bounding boxes, ground-plate positions, and annotator labels.
DANDI Archive for NWB datasets
DANDI is a BRAIN Initiative archive for publishing and sharing neurophysiology data, including electrophysiology, optophysiology, and behavioral data packaged as NWB and related standards.
International Brain Laboratory public data
The International Brain Laboratory public data releases expose standardized mouse decision-making experiments, including Neuropixels recordings, widefield calcium imaging, behavior, and session metadata accessed through the ONE API.
OpenNeuro
OpenNeuro is a free, open platform for sharing neuroimaging datasets, with public search, dataset pages, and download paths for web, S3, DataLad, and the OpenNeuro CLI.